Unit 2 Bio Notes PDF

Helicase starts by separating the leading and lagging strands and unwinds them The binding proteins keep them separated Dna primase adds an RNA primer to the DNA strand so the polymerase can attach on DNA polymerase replicates the DNA by adding complementary nucleotides to the template strand. It...

Helicase starts by separating the leading and lagging strands and unwinds them The binding proteins keep them separated Dna primase adds an RNA primer to the DNA strand so the polymerase can attach on DNA polymerase replicates the DNA by adding complementary nucleotides to the template strand. It can only go from 5’ to 3’ first in the leading strand. In the lagging strand, it is split into okizaki fragments where the primer can be attached and then the DNA polymerase replicates. Nucleotide replacement enzyme then replaces primer with correct nucleotide Ligase on lagging strand seals the gaps caused by the okizaki fragments. Topoisomerase unwinds the DNA. 5’ end has free phosphate group, 3’ end has free hydoxyl group, enzymes can only be added to the hydroxyl group on 3’ end Purines are adenine and guanine while pyrimidines are cytosine and thymine. Aeneince and thymine pair while Cytosine and Guanine pair. -DNA is very tightly packed together for cell division. -Transcripiton and translation: DNA is transcripted into RNA and RNA is then translated into Protein. Genes are genetic code which tells what amino acids, out of 20, should be made. -Gamow invented the idea that a 3 letter code would encrypt to a amino acid sequence. A codon table tells which genetic codon encodes for which type of amino acid. -Mutations are changes in DNA sequence due to replication errors or mutagens which are other environmental factors. Base subsitution is when a nucleotide is replaced with another and therefore impacts what code is transcribed as. Deletion or insertion shifts all the nucleotides which greatly affects the transcription. A single base substitution causes sickle cell armenia. Class 2 -Transcriptions happens first where DNA code is transcripted by genes into messenger RNA -Translation happens 2nd and involves transfer RNA converting a unique nucleotide codon into unique amino acids. -DNA has thymine as a nitrogen base but RNA has a Uracil base instead, the both have A, G, and C. -For the sugars DNA has Deoxyribose and RNA has ribose, the both have phosphate. -DNA is double stranded but RNA is single stranded. -RNA is much more diverse usage than DNA as it can conform to a variety of shapes. Exons and Introns- Occurs in Eukaryotic DNA and introns are removed from the genes leaving just the exons to be pushed together and then to be transcribed. The introns are then broken down and reused. Spliceosome is responsible for cutting out the introns and leaving the sequence of exons. Eukaryotes -GTP cap is attached to 5’ end to prevent degradation and 3’ end serves to export the signal. DNA transcribed->RNA transcript-> GTP Cap and poly A tail Added-> Spliceosome cuts out introns-> Final mRNA transported to cytoplasm. Mutations and repairs -Specialized enzymes fix specific errors such as mismatch repair. Other ones are changes to nucleotides caused my environmental factors. Some causes of issues cause different difficulty in repairing the DNA. Karyotype-# of chromosomes in nucleus of normal eukaryotic cell. Humans have 22 pairs of autosomal chromosomes and 1 pair of chromosomes. The diploid number of chromosomes in humans is 46 and the haploid number is 23. Haploid is sex cells which is why they have the xx or xy chromosomes. -Dominant genes are upper case and recessive are lower case. If the mother or father have a dominant allele, then the offspring will get that trait. Mitosis: Occurs during cell divisions and are important for cell repair and growth. Occurs in somatic cells with divide the diploid complement into the daughter cells. Is followed by cytokinesis which divides the cytoplasm, organelles, and cell membranes equally into the 2 daughter cells. Meiosis: Occurs in sex organs which produces haploid gametes. Produces zygotes which has same DNA as each other. PMAT Mitosis: Prophase- chromosomes condense, metaphase- chromosomes line up in middle, Anaphase- chromatids are pulled away to opposite sides, Telophase- cell starts to split in 2, Cytokinesis- New membranes are formed leaving 2 diploid cells which are the exact same as the starting cell. PMAT Meiosis:Prophase- chromosomes join up with homologous pairs and can crossover, Metaphase- chromosomes line up in pairs in middle, Anaphase- Chromosomes are pulled to opposite sides, Telophase- Gene regulation- Even though each cell has same DNA, makes sure certain proteins are produced only in certain parts where it is needed. Like HCL being made in stomach and not in the eyes. RNA polymerase starts transcription starts at a promoter, but operators have the ability to be attached to represssors that can stop the transcription if there is no need to make an enzyme in that current environment. Lac operon stops production of enzymes to break down lactose if no lactose is in the environment because the repressor has nothing to bind to. Eukaryotes gene regulations: -DNA packing prevents access of DNA for transcription -Have enhancers and silencers; enhancers are where transcription factors, proteins that help RNA bind to promoters, can bind. Homeodomain proteins are coded for by HOX genes during development, which turn on and off genes in certain areas of the body that need to be made. HOX genes are the same in all organisms, from flies to humans. HOX genes specify where body parts should be made. -Alternative RNA splicing splits up into many mRNAs. -MicroRNA and RNA interference -Translation and after is also regulated Epigenetics: study of heritable changes in gene expression. Epi occurs in the external genome, not the nucleotides and actual genotype. Impacts how cells read the genes and expressed, but not the actual genes. Methyl groups tell a gene whether to be expressed or not. Epigenome changes throughout life because of conditions, like puberty or environmental factors. Epigenetics can be passed down. Acetyl groups attach to histones and impact histone packaging, which can make them more accessible. Small RNA molecules can attach to DNA, which can turn genes on or off. RNA Interference: RNA molecules with proteins can destroy mRNA molecules before they reach ribosomes and will suppress the expression of certain genes. This is because they are thought of as viruses, so they are destroyed. miRNA silences many genes, while siRNA only silences very specific genes. mRNA-messenger RNA. rRNA-ribosomal RNA tRNA: Transfer RNA snRNA: Forms the spliceosome, which removes introns from RNA. miRNA- silences many genes siRNA silences specific genes. Class 4 Omic sciences: genomics, epigenomics, proteomics (gene products), interactomics (interaction between molecules), and metabolics (determine function). -Sanger sequencing method-invented dna sequencing to figure out sequence of nucleotides, for example, insulin. Takes advantage of special nucleotides that are midding OH on 3’ end. These dont allow DNA polymerase on it and grow the strand. These are called ddNTP. Destrand DNA to single strands-> you have DNA Polymerase and dATP, dCTP, dTTP, and dGTP and a primer-> put all the stuff in 4 different tubes, separated by the 4 bases-> then grow the complementary strands in the tubes of the nucleotides-> separate the old strands and new strands-> do the electropherese Shotgun Sequencing: We cut the long original DNA into random short fragments, Human Genome Project: First major DNA project to determine sequence of all DNA in the human genome. In 2003, entire version was created with results. Only 1.5 percent are exons that code for proteins. Project Encode: Now that we know what the nucleotide sequences are, what do they actually encode for. Assigns function to the genome. Found 80% of genomes continas RNA molecules with biochemical function, so they arent junk. RNA is a major functional unit of the epigenome. Evolution can occur by selection for RNA sequences that alter gene regulation. Found 90% of DNA mutations for disease fell into gene switching areas for epigenome. Genome 10k project: sequence DNA of at least 10000 vertebrates. The roadmap Epigenomics Project: Wanted to find switches caused by tags of epigenome that caused diseases. Epigenome Changes and Disease: Not single modifications that cause diseases, but many changes in a certain way cause the changes in gene expression and then disease. Epigenome Changes and Development: Enhancers activated through interactions with transcription factors. Epigenomic changes can have a large impact on development and regulation. Earth Biogenome Project: Goal to sequence all eukaryotes Genetic Origin of Disease: Chromosome number alterations. Nondisjunction: Failure of chromosomes or chromatids to separate during meiosis. Fertizilation after nondisjuction results in zygotes with the wrong number of chromosomes. Nondisjunction in meiosis produces no normal chromosomes, 2 with 3 and 2 with 0. Nondisjunction in meiosis two produces 2 correct gamets, and one with 3 and one with 1. An extra copy of chromosome 21 causes Down syndrome. XYY: Most men have XY chromosomes, but a person with XYY was found. About 1 in 1000 men have XYY, but it was found that the extra Y doesn’t make them more dangerous or criminal as they were once thought to be. Klinefelter syndrome: Males have an extra X, which causes low testosterone and low fertility. Turner Syndrome: Female with a missing X, which causes short stature, a broad chest, and ovaries that don't work. Dominant Autosomeal Disorder: Children with a father having it will have a 50% chance of having the disease. Recessive Autosomeal Disorder: Only occurs if both mother and father have the recessive gene. X-linked disorder: caused by an X-linked chromosome. Unit 2 Class 5- Personalized Medicine -Early screening and detection, which can cause prevention -More effective medications and vaccines for a specific person based on their genes. - Newborns can have genes sequenced to figure out mystery conditions in less than a day. - A SNP is an area within chromosomes where if a gene has a mutation than it causes a disease or effect. This is data used in genome wide studies. -Microbiome: Detects, prevents, and diagnoses infections or diseases. Aims to replace bacteria that contribute to the disease in the microbiome. -Pharmacogenomics: Use patients genomes to predict drug efficacy and dosage. Can show how your body will have side effects to certain medications. -Clinomics: Accurate interpretation of the genomic data to guide decisions about help. -Epigenomics: Looks at which factors act on individual genes and how it will affect our help. Personalized medicine and Cancer: Mutations in one single cell that continuously divides. 100 types of cancer caused by different genetic changes. Epigenome affects cancer but unknown how much. All cancers are genetic diseases. -Usually occurs from multiple mutations in a cell and usually associated with somatic cells(not reproductive). Typically not from the germline and usually from epithelial (surface) cells. -Oncogenes: Proto-oncogenes stem cell division but cause issues when it develops into an EGFR (an oncogene) instead of normal division. This causes mutated genes to divide and grow a lot. -Tumor Supressor Genes (TSG): Normally regulated growth so theres not too much division, but when its mutated defective proteins grow out of control. Cancer Genome Project: Found that there’s many types of tumors and not one type of cancer. So drugs must target specific profiles for every individual. Identifies genotype of each type of cancer and how the mutation occurs and therefore treatment for it. Breast Cancer: Most common cancer. 4 genetic disease types have been found. The tissue of it does not define the genetic profile, such as one type of it is similar to ovarian cancer. Treatment changes based on the specific person and their cancer. Cancer conclusions: caused by 2-8 sequential alterations, 140 genes are known to where mutations cause cancer, every individual tumor is distinct due to their alterations. Genomic Testing for Prevention: BRCA2 and BRCA2 genes repair damaged genes but can have insertions or deletions that decrease their abilities, which increases likelihood of cancer. They are normally expressed in breast and other tissues. Class 6 -Cancer Therapies: Hormone Therapy: uses synthetic or natural hormones to add, block, or remove hormones from the body to stop the growth of cancer cells. Signal transduction inhibitors: are substance that block signals from cells, which can affect cell division and cell death and also kill cancer cells. Angiogenesis inhibitor: Inhibitors that stop the growth of blood vessels to the tumor so it doesn’t grow. Immunotherapies: uses T-cells (white blood cells) from patients to make lab-grown ones to improve how the immune system works to destroy cancer cells. Monoclonal antibody: a type of immunotherapy that is specific to certain cell types and has an immune system that attacks only specific cancers. New Frontiers: CRISPR: cas genes code for helicases and nucleases that cut dna, CRISPRS contain spacers that contain old genetic information for old diseases, the CRISPRS are in bacteria in the immune system that form crRNA, which combines with tracrRNA to make gRNA that cuts DNA at specific parts Stem Cells: cells that don’t have a specific function but can be used as all the other types of cells in the body. They regenerate body parts by replacing defective cells with stem cells. Adult stem cells were shifted to IPSC cells which are differentiated from its initial state. Like if an adult stem cell is developed in skin, it can be turned into IPSC that can be used the same as embryonic stem cells. Synthetic Biology: A new area that applies engineering principles to biology. EIDS (Emerging Diseases): Caused by changes in population growth in new areas, more contact with animals, behaviors of people, travel, changing ecosystems. Epidemics affect a large number of people in one area, pandemics have spread to more than one area. Zoonotic diseases are from other vertabrates, usually direct contact between animals and humans RNA viruses have very high mutation rates which causes high transmission rates. Viruses and vaccines: traditional vaccines used dead or disabled virus, some use a toxin, some use small part of virus, they all require growth and transport of blood pathogens. The new mRNA vaccines by making the RNA that the virus has so the body recognizes it, DNA vaccines uses the dna which is much more stable in a carrier virus, but the carrier virus will need to be updated often. Antiobiotics